Effects of Bowel Flora on Wellbeing

The ecosystem that lives in your gut is complex, dynamic, amazonian in scale  and poorly understood. It’s affected by genes and what we put in our mouths: food, bacteria, probiotics and antibiotics. A recent study on mice has confirmed  some long held suspicions of patients and clinicians alike.



Rough Summary

Some strains of mice are more resistant to a particular bacterial gut infection, however a genetic cause has not yet been found. Researchers eliminated the gut flora from a susceptible strain of mice and gave them a bowel flora transplant from resistant mice. They then challenged these recipients with the pathogen and found resistance was conferred, temporarily.

Several things we can take from this, relevant in man and animal, much of which you may have already guessed:

1. Gut flora varies between individuals, and will change over time.  This variation will be controlled by genes, the interactions between bacteria that colonise our gut during our lifetime, probably diet and definately antibiotics.

2. This difference between our gut bacteria may make us more or less susceptible to specific bowel pathogens. It may also account for  a proportion of the the well-known ‘sensitive tummy’ patients  (Irritable bowel etc) that vets and doctors see.

Irritable Bowel Syndrome is a ‘dustbin diagnosis’: when all the other diseases are ruled out, the remaining patients are  grouped as IBS.  As a gastroenterologist once admitted – there are proably 10 or more unknown diseases currently lumped together as IBS, awaiting medical understanding. Intestinal flora dysbiosis is bound to be involved in the pathogenesis of some of these diseases of the future.

3. In these mice, the bowel transplant lasted for about 1 month, so there may be a limit to the extent we can permanently modify our gut flora without repeated inoculations.

And the implications:

1. Don’t use antibiotics unnecessarily, and keep to a narrower spectrum. Nothing ground-breaking here.

2. Observe your pet’s reaction to dietary change and antibiotics. This type of  empiric information  is totally invaluable to your vet or doctor.

3. If our bowel flora is disturbed, by a rotten bone, antibiotic course or other medication, it may be several months before the bacterial populations return to some sort of new steady-state. This may partly explain the common post-infectious IBS patient.

4. Whilst there is no doubt that a significant proportion of patients with diarrhoea respond spectactularly to empiric antibiotic treatment, there’s also the likelyhood that the recovery of some patients may be slowed. Our use of antibiotics is often crude, and use of broad-spectrums is like throwing a hand-grenade into a room of people and expecting it to just kill just your enemy. Like civilians in a war zone, innocent bowel flora are often the ‘collateral damage’ when waging war on infection with antibiotics.

My Questions:

1. While enzymic depletion and the ‘leaky gut‘ thesis may explain some food intolerances that develop after bowel infection, how do chronic, subclinical changes in flora interact with the development of food allergies and intolerances?

2. Many of us now use probiotics. Some are monovalent, some poly.  Some give probiotics intended for humans to their dogs.  All are created in an industrial fashion, and in no way resemble the ‘perfectly balanced bowel flora’ for our unique genetic make-up. Can this one-shoe-fits-all approach really be expected to work? This issue may explain the patchy results of controlled trials with probiotic therapy.

3. Coprophagia is a common behaviour in dogs. Is this a form of probiotic self-medication? Or is it just a fetish for the street-truffle?



  • A recent study published in Nature found humans could be categorised as one of three ‘Enterotypes’, not unlike the bloodtype categories discovered decades ago. It’s likely that treatments of the future will be tailored to your not-so-unique bowel ecosystem. The NY times article expounds the significance further.


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One Response to “Effects of Bowel Flora on Wellbeing”

  1. VOS says:

    Hi Matt;
    Always reading!
    My 2 Dalmation males, r fed
    “apple cider vinegar” & ‘greek yoghurt’
    with green vegetables & heaps of fruit with the meat.
    to keep the breath sweet & fresh.
    in particular the Boys like to eat a lot of Horse manure!!!
    Love your work

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